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Bug in rheo, cleaning up old files

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This commit is contained in:
jtclemm
2023-10-30 20:22:14 -06:00
parent 5986fb90b9
commit 0945c3dda8
3 changed files with 2 additions and 248 deletions
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4
src/RHEO/fix_rheo.cpp
View File

@ -94,11 +94,11 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"surface/detection") == 0) {
surface_flag = 1;
if(iarg + 2 >= narg) error->all(FLERR,"Illegal surface/detection option in fix rheo");
if (strcmp(arg[iarg + 1], "coordination")) {
if (strcmp(arg[iarg + 1], "coordination") == 0) {
surface_style = COORDINATION;
zmin_surface = utils::inumeric(FLERR,arg[iarg + 2],false,lmp);
zmin_splash = utils::inumeric(FLERR,arg[iarg + 3],false,lmp);
} else if (strcmp(arg[iarg + 1], "divergence")) {
} else if (strcmp(arg[iarg + 1], "divergence") == 0) {
surface_style = DIVR;
divr_surface = utils::numeric(FLERR,arg[iarg + 2],false,lmp);
zmin_splash = utils::inumeric(FLERR,arg[iarg + 3],false,lmp);

200
src/atom_vec_rheo_thermal.cpp
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@ -1,200 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
Joel Clemmer (SNL), Thomas O'Connor (CMU), Eric Palermo (CMU)
----------------------------------------------------------------------- */
#include "atom_vec_rheo_thermal.h"
#include "atom.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
AtomVecRHEOThermal::AtomVecRHEOThermal(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = Atom::ATOMIC;
mass_type = PER_TYPE;
forceclearflag = 1;
atom->status_flag = 1;
atom->conductivity_flag = 1;
atom->temperature_flag = 1;
atom->heatflow_flag = 1;
atom->pressure_flag = 1;
atom->rho_flag = 1;
atom->viscosity_flag = 1;
// strings with peratom variables to include in each AtomVec method
// strings cannot contain fields in corresponding AtomVec default strings
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = {"status", "rho", "drho", "temperature", "heatflow", "conductivity", "pressure", "viscosity"};
fields_copy = {"status", "rho", "drho", "temperature", "heatflow", "conductivity", "pressure", "viscosity"};
fields_comm = {"status", "rho", "temperature"};
fields_comm_vel = {"status", "rho", "temperature"};
fields_reverse = {"drho", "heatflow"};
fields_border = {"status", "rho", "temperature"};
fields_border_vel = {"status", "rho", "temperature"};
fields_exchange = {"status", "rho", "temperature"};
fields_restart = {"status", "rho", "temperature"};
fields_create = {"status", "rho", "drho", "temperature", "heatflow", "conductivity", "pressure", "viscosity"};
fields_data_atom = {"id", "type", "status", "rho", "temperature", "x"};
fields_data_vel = {"id", "v"};
setup_fields();
}
/* ----------------------------------------------------------------------
set local copies of all grow ptrs used by this class, except defaults
needed in replicate when 2 atom classes exist and it calls pack_restart()
------------------------------------------------------------------------- */
void AtomVecRHEOThermal::grow_pointers()
{
status = atom->status;
conductivity = atom->conductivity;
temperature = atom->temperature;
heatflow = atom->heatflow;
pressure = atom->pressure;
rho = atom->rho;
drho = atom->drho;
viscosity = atom->viscosity;
}
/* ----------------------------------------------------------------------
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
------------------------------------------------------------------------- */
void AtomVecRHEOThermal::force_clear(int n, size_t nbytes)
{
memset(&drho[n], 0, nbytes);
memset(&heatflow[n], 0, nbytes);
}
/* ----------------------------------------------------------------------
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecRHEOThermal::data_atom_post(int ilocal)
{
drho[ilocal] = 0.0;
heatflow[ilocal] = 0.0;
pressure[ilocal] = 0.0;
viscosity[ilocal] = 0.0;
conductivity[ilocal] = 0.0;
}
/* ----------------------------------------------------------------------
assign an index to named atom property and return index
return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */
int AtomVecRHEOThermal::property_atom(const std::string &name)
{
if (name == "status") return 0;
if (name == "rho") return 1;
if (name == "drho") return 2;
if (name == "temperature") return 3;
if (name == "heatflow") return 4;
if (name == "conductivity") return 5;
if (name == "pressure") return 6;
if (name == "viscosity") return 7;
return -1;
}
/* ----------------------------------------------------------------------
pack per-atom data into buf for ComputePropertyAtom
index maps to data specific to this atom style
------------------------------------------------------------------------- */
void AtomVecRHEOThermal::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
if (index == 0) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = status[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = rho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = drho[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = temperature[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 4) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = heatflow[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 5) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = conductivity[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 6) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = pressure[i];
else
buf[n] = 0.0;
n += nvalues;
}
} else if (index == 7) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
buf[n] = viscosity[i];
else
buf[n] = 0.0;
n += nvalues;
}
}
}

46
src/atom_vec_rheo_thermal.h
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@ -1,46 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef ATOM_CLASS
// clang-format off
AtomStyle(rheo/thermal,AtomVecRHEOThermal);
// clang-format on
#else
#ifndef LMP_ATOM_VEC_RHEO_THERMAL_H
#define LMP_ATOM_VEC_RHEO_THERMAL_H
#include "atom_vec.h"
namespace LAMMPS_NS {
class AtomVecRHEOThermal : virtual public AtomVec {
public:
AtomVecRHEOThermal(class LAMMPS *);
void grow_pointers() override;
void force_clear(int, size_t) override;
void data_atom_post(int) override;
int property_atom(const std::string &) override;
void pack_property_atom(int, double *, int, int) override;
private:
int *status;
double *conductivity, *temperature, *heatflow;
double *pressure, *rho, *drho, *viscosity;
};
} // namespace LAMMPS_NS
#endif
#endif